Genotype-Phenotype-Environment Associations and Potential Local Adaptation Signals in the Mesquite Lizard Along the Eastern Trans-Mexican Volcanic Belt.

Anthropogenic activities modify the composition and configuration of landscapes and fragment habitats, generating environmental gradients and dispersal barriers that alter gene flow and generate selective pressures. Identifying local adaptation, which depends on the balance between selection and gene flow, requires integrative approaches that combine multiple sources of evidence. Notably, signals of local adaptation have been poorly evaluated in Neotropical lizards. By integrating phenotypic, genomic, environmental, and landscape data, we assessed whether the mesquite lizard Sceloporus grammicus exhibits morphological changes associated with landscape variables, and also potential signals of local adaptation along a natural-anthropogenic gradient across the eastern Trans-Mexican Volcanic Belt. Phenotypic results showed traits that varied with landscape variables, including a negative effect of elevation on snout-vent length (SVL) and a positive effect of distance to forested areas (Dfz) on body condition index (BCI). Using genotype-environment and genotype-phenotype associations, we detected 72 candidate single nucleotide polymorphisms (SNPs) with adaptive signals, based on which we identified four adaptive units across the study area. Functional enrichment highlighted four genes (ADCY10, LMOD3, NINJ1, STX16) with overrepresented molecular functions. The frequency of the alternative allele in SNPs annotated to ADCY10, LMOD3, and NINJ1 increased with elevation and in individuals with smaller SVL, while it increased with Dfz and BCI for STX16. Overall, our results support spatially structured, landscape-linked candidate adaptive variation consistent with previously inferred functional connectivity patterns for the mesquite lizard. They also suggest mechanisms for exploring physiological and metabolic responses under environmental heterogeneity and anthropisation that could favor local adaptation.